Morphogenesis is a fundamental process in a wide range of cell functions and therefore one of the best studied. Consequently, most of the contributing component processes and the majority of their molecular parts are known. Much less understood is how the many underlying component processes are integrated into a working whole. This integration is regulated by a system of chemical and mechanical pathways with i) a high level of non-linearity; ii) a high level of redundancy; and iii) a separation in space and time of cause and effect between component processes. A key consequence of such a pathway configuration is that perturbation of any component can lead to wide-ranging and fast adaptation. Hence, phenotypic changes primarily reflect a reconfiguration of the system and not necessarily the function of the perturbed target. This challenge has plagued the interrogation of molecular functions in cell morphogenesis, and has led to numerous controversies that likely relate to slight differences in experimental designs triggering divergent adaptation processes. To circumvent some of these limitations, my lab has developed over the past 10 years quantitative live cell imaging methods that reveal the functional interplay between spatially and temporally distributed molecular processes, such as cytoskeleton polymer dynamics, forces, and chemical signals, based on the coupling of their spontaneous activation fluctuations in unperturbed systems. Building on key discoveries of cell morphogenic control mechanisms, which required the use of a perturbation-free approach rather than a more conventional experimental paradigm, we propose here an extension of this research program that will introduce a rigorous statistical framework to infer the coupling of molecular processes in cause and effect cascades. This includes algorithms to identify directly, from fluctuation time series, feedback interactions between processes and the dynamic rewiring of the cause and effect cascades under variable cellular conditions. These computational developments will be paralleled by innovation in experimental systems for multispectral live cell imaging of up to 8 concurrent processes and for the analysis of cell morphogenesis in native tissue environments in 3D. The studies will be focused on the coordination of the system of highly redundant actin modulating factors in promoting actin mediated cell shape changes and the interactions of this system with the regulatory system of RhoGTPase signals. The impact of this work will reach far beyond the new insights we will gain of the regulation of these pathway systems. The work will address the notorious adaptation responses of complex molecular systems, which are generic and a fundamental impediment to the systematic inquiry of cell functions. The tools we develop to overcome some of these problems will be made available as widely-adoptable approaches to the analysis of cell regulatory processes.